I finally figured it out. Apparently the tonneau cover motor slide back over the years causing the problem I/we had. This is what you do:
1. Take the cover out to expose the tonneau motor inside the trunk.
2. Pic 1 & 2 - Loosen the top and bottom two nuts that hold the assembly in place. Also, that bar across that you see in the first picture is what brings the tonneau cover up, take the clip out and unhook it from the motor.
3. Pic 3 - Take the bulb out of the stop light so you don't break it in your next step.
4. Pic 4 - Use a pry bar or something similar to push the motor forward and then secure the nuts tightly.
5. Pic 5 - Now I have about 3/4 in of clearance on the tonneau cover.
IMP Note: In order to put the bar on the motor you took out earlier, you have to able to open just a little the tonneau cover with the trunk open (remember is not going to open because you unhooked it from the motor earlier).
--What you do is: close the truck latch with a screw driver and find the push switch that activate the truck lights and keep it press in (you can have somebody do this one for you). This will tell the convertible circuits that the trunk is close and is save to open the top.
--Now, you hit the switch to open the top until you see it disengage and you are able to open it with your hands (it happens really fast). Then, with one hand open the cover until the bar line up with the motor pin where you took it out, push it in and replace the clip and you set. Now close the trunk the right way and try it out. You should get the same clearance I got. Good luck.